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2: Chemistry and Biologically Important Molecules

  • Page ID
    2606
    1. Molecular Hierarchy of Life:

    A. subatomic particles->atoms->molecules-> cellular structures->cells

    II. Atoms

    A. Atomic subunits: protons, neutrons, electrons. atomic number, atomic mass, isotopes

    B. Electron shells

    C. Biologically important elements: CHONPS

    III. Chemical Bonds

    A. Chemical bonds/attractive forces: attractive forces between atoms. Number of electrons in outermost energy level /shell determines chemical properties of an atom. If outer (=valence) shell is full of electrons, atom does not tend to react with other atoms. If valence shell is not full, atom tends to react with other atoms to fill valence electron shell.

    Three types of bonds/attractive forces: Type of bond formed depends on electron configuration and electronegativity of atoms involved:

    1. ionic bonds: sodium and chloride ions. Sodium atom (11 p+, 11e-) loses 1 electron and becomes positively charged cation. Chloride atom (17 p+, 17 e-) gains 1 electron and becomes negatively charged anion.

    Oppositely charged sodium and chloride ions attracted to each other. Electrical attraction between 2 oppositely charged ions is an ionic bond.

    2. covalent bonds: formed when atoms share pairs of electrons to fill valence shell. Number of covalent bonds formed depends on valence electrons. single, double, triple covalent bonds. e.g. H2O. Indicated by solid line “-“

    a. electronegativity: - atoms ability to attract electrons. low= H, C; high=O

    b. polar covalent bond: 2 atoms unequally share electrons; one member carries slight positive charge, one member carries slight negative charge. eg water

    partial charge=δ

    c. nonpolar covalent bond: 2 atoms equally share electrons. Charge evenly distributed. eg hydrocarbons

    electronegativity

    nonpolar covalent bonds

    polar covalent bonds

    partial δ -/ partial δ +

    C=2.5

    C-H

    O-H

    H=2.2

    H-H

    N-H

    O=3.5

    O=O

    O=C

    N=3.1

    N=N

    O=P

    P=2.1

    C-C

    N-C

    S=2.4

    If difference of electronegativity is approx >0.5, covalent bond formed will be polar

    3. Hydrogen "bonds" (“...”): Not true bonds,; an attractive force. Hydrogen involved in a polar covalent bond carries a partial δ positive charge. The hydrogen may also be attracted to other molecules carrying a partial δ negative charge, forming hydrogen bond.

    H...N H...O

    δ+ … δ- δ+… δ -

    Bio 440 Chemical Bonds/attractive forces concept map : distribute in lecture

    Text Box: Covalent bonds
-indicated by solid straight line_   -    
Text Box: Polar Covalent bonds -result in partial negative δ-   and partial positive δ+   charges
e.g δ- O—Hδ+       δ- N—Hδ+        δ- O—Pδ+
Text Box: >Bond strength in aqueous environments strongest  covalent>ionic>H bonds weakest

>Water is attracted to substances with full electrical charges (ions) or polar covalent bonds
>   such substances are called “hydrophilic”

>Nonpolar bonds/substances lack electrical charge, consequently water is not attracted-
   >such substances are called “hydrophobic”


File:/C:\Users\Jim_Horst\AppData\Local\Packages\oice_15_974fa576_32c1d314_44e\AC\Temp\msohtmlclip1\01\clip_image007.pngFile:/C:\Users\Jim_Horst\AppData\Local\Packages\oice_15_974fa576_32c1d314_44e\AC\Temp\msohtmlclip1\01\clip_image008.pngText Box: “Hydrogen Bonds”
Weak attractive forces between atoms involved in polar covalent bonds   
 H bond= ---              
  δ- O—Hδ+ ---  δ- O—Hδ+
H bond
δ- N—Hδ+ ---  δ- O—Hδ+ 


File:/C:\Users\Jim_Horst\AppData\Local\Packages\oice_15_974fa576_32c1d314_44e\AC\Temp\msohtmlclip1\01\clip_image010.pngFile:/C:\Users\Jim_Horst\AppData\Local\Packages\oice_15_974fa576_32c1d314_44e\AC\Temp\msohtmlclip1\01\clip_image011.pngText Box: Electronegativity is significantly differentFile:/C:\Users\Jim_Horst\AppData\Local\Packages\oice_15_974fa576_32c1d314_44e\AC\Temp\msohtmlclip1\01\clip_image013.pngText Box: Nonpolar covalent bonds  -
e.g.  C-C    O=O      H-H    C-H
File:/C:\Users\Jim_Horst\AppData\Local\Packages\oice_15_974fa576_32c1d314_44e\AC\Temp\msohtmlclip1\01\clip_image015.pngFile:/C:\Users\Jim_Horst\AppData\Local\Packages\oice_15_974fa576_32c1d314_44e\AC\Temp\msohtmlclip1\01\clip_image016.pngText Box: EN electronegativity is same or similarFile:/C:\Users\Jim_Horst\AppData\Local\Packages\oice_15_974fa576_32c1d314_44e\AC\Temp\msohtmlclip1\01\clip_image018.pngText Box: Electrons are sharedFile:/C:\Users\Jim_Horst\AppData\Local\Packages\oice_15_974fa576_32c1d314_44e\AC\Temp\msohtmlclip1\01\clip_image020.pngText Box: Ionic bonds
-attraction between oppositely charged ions
File:/C:\Users\Jim_Horst\AppData\Local\Packages\oice_15_974fa576_32c1d314_44e\AC\Temp\msohtmlclip1\01\clip_image022.pngText Box: Electrons are transferred between atoms ->forms charged ions
cations+   -anions   e.g. Na+  -Cl


File:/C:\Users\Jim_Horst\AppData\Local\Packages\oice_15_974fa576_32c1d314_44e\AC\Temp\msohtmlclip1\01\clip_image024.pngText Box: Electrons are …..File:/C:\Users\Jim_Horst\AppData\Local\Packages\oice_15_974fa576_32c1d314_44e\AC\Temp\msohtmlclip1\01\clip_image026.pngText Box: Chemical bonds/attractive forces

    B. Bond strength in aqueous solutions: strongest covalent> ionic> H bond weakest

    1. Although weak, multiple hydrogen bonds are important in stabilizing the three-dimensional shape of many biological molecules. (Shape determines function “functional conformation”)

    2. Covalent bonds are usually very stable

    -cells use protein catalysts called enzymes to “break” covalent bonds e.g. hydrolysi

    3. Ionic compounds “fall apart” in water. ex NaCl crystals in water; ions attracted to polar water molecules

    IV. Special Properties of Water

    Most microorganisms contain approx. 70% water. Most chemical reactions occur in aqueous environments

    Key to unique properties of water: polarity of water molecule and hydrogen bond formation with other water molecules

    1. cohesion/adhesion

    2. less dense as solid (ice) than liquid therefore ice floats-> oceans/lakes habitable in cold climates

    3. high specific heat/water absorbs lots of energy before enough H bonds are broken t increase kinetic energy/velocity of water molecules leading to increase temperature. Water helps moderate temperature changes.

    4. high heat of vaporization/as water evaporates, removes energy/heat-> cooling effect

    5. excellent solvent=polar molecule

    hydrophilic substances=water “loving”, polar/ionic substances; water molecules attracted to, form bonds with hydrophilic substances

    hydrophobic substances=water “hating”; noncharged, nonpolar, do not dissolve in /mix with water; since these substances lack charges, water molecules are not attracted to them e.g hydrocarbons, lipids

    6. water ionizes: H2O <-> H+ + OH-

    7. Water and acid-base balance. pH (also Ch 4 in lab manual)

    pH= -log [H+] (more in lab)

    acids: fig ___-acids ionize, release free H+, increase H+ concentration of aqueous solution

    bases: lower H+ concentration of aqueous solution (strong bases ionize releasing hydroxyl ions OH- e.g. NaOH-> Na+ + OH-; weak bases bind free hydrogen ions/protons H+ e.g. ammonia NH3 + H+-> NH4+

    V. Functional Groups and Carbon skeletons

    A. Organic chemistry: study of carbon containing compounds (excluding inorganic CO2)

    1. carbon/carbon skeletons: ability to form 4 covalent bonds/endless variety of carbon skeletons

    -variations of carbon number, branching, double bonds, ring formation

    -examples; hydrocarbons, = H and C only; nonpolar: methane, ethane

    2. adding functional groups to carbon skeletons changes character of molecule; most often chemical reactions involve functional groups

    B. Functional Groups: (R=”rest” of molecule/carbon skeleton)

    methyl: nonpolar, hydrophobic R-CH3

    hydroxyl: polar, hydrophilic R-OH

    carbonyl C=O : polar, hydrophilic

    terminal carbonyl: aldehydes: R-CH=O

    internal carbonyl ketone: R1-CO-R2

    carboxyl: polar, hydrophilic, acidic/ionizes to increases free H+ in solution

    amino: polar, hydrophilic, basic, binds H+, decreases free H+ in solution

    phosphoric acid residue (very acidic)->ionizes->phosphate: polar, hydrophilic,

    VI. Biologically Important Molecules: proteins, nucleic acids, carbohydrates, lipids

    (see chem. homework sheet )

    A. Macromolecules= “large molecules”

    1. most are polymers of repeating subunits (monomers)

    -joined by removal of H + OH = water : “dehydration synthesis” or “condensation reactions” (opposite=hydrolysis)

    A-H + OH-B--> -dehydration synthesis--> A-B + H2O

    <hydrolysis<-

    2. polymers: subunits

    a. proteins/amino acids

    b. nucleic acids/nucleotides

    c. carbohydrates: polysaccharides/monosaccharides “sugars”

    3. Lipids=hydrophobic

    B. Proteins: polymers of amino acids

    1. Amino acids: ~20 different types/all share basic structure:

    -central carbon with 4 “groups” attached; H, carboxyl group, amino group and R side group.

    ~20 different R side groups ;

    -R groups specify “personality”/chemical reactivity of amino acid.

    -Amphoteric: has both acidic and basic qualities

    -Proteins contain L isomers only

    .( Bacterial cell walls/some antibiotics contain D amino acids; these are NOT proteins).

    -Bacteria have formyl-methionine f-met as 21st amino acid

    2. Polymers of amino acids: aa1-aa2-aa3-aa4-aa5-aa6---- linked by peptide bonds

    3. most abundant component of cells (next to water) 50% of dry weight=protein

    4. Functions:

    a. enzymes= protein catalysts/speed up chemical reactions without being “used up” -biochemical “tools” of cells; active site=substrate specific

    b. structural proteins

    c. transport proteins d. receptors, antibodies, chemical messengers and more....

    5. Protein structure: primary, secondary, tertiary, quaternary.

    Levels of protein structure

    Primary structure: specific sequence of amino acids in polypeptide chain

    -covalent peptide bonds

    -determines all other higher levels of structure thus determines “functional conformation”

    -amino acid sequence of a protein is determined by the DNA nucleotide base sequence of its gene

    Secondary structure; coiling/folding of polypeptide chain into specific patterns such as alpha α helix /β pleated sheets

    -hydrogen bonds between members of peptide “backbone” (R groups not involved)

    Tertiary structure: additional folding of polypeptide into complex 3-D shape- for many proteins, the functional conformation. R group interactions (H bonds, ionic, covalent bonds, hydrophobic interactions, London Dispersion Forces/van der Waals forces; disulfide bridges between cysteine residues)

    Quaternary structure: the association of 2 or more polypeptide subunits to form functional protein. ex hemoglobin, immunoglobulin. R group interactions as for tertiary structure

    6. Protein Denaturation: unfolding of polypeptides. Loss of shape/structure=loss of function

    -high temperature, pH extremes, heavy metals, alcohols.

    -applications: protein denaturation is used to inactivate/kill pathogenic microbes.

    - autoclave, boiling, alcohols, heavy metals, physical "abuse"

    -Usually denaturation is irreversible.

    -Exceptions: thermophiles, chaperone proteins.

    7. “Protein mis-folding diseases”: abnormally folded prion proteins cause TSE, Transmissible Spongiform Encephalopathies. The disease-causing prions are incredibly difficult to denature, resist denaturation by cooking, normal autoclaving, most chemicals. Most resistant biological structures known. Additional protein mis-folding disease: Alzheimer's, Parkinsons, more (could Alzhemimer's, Parkinson's diseases be transmissible as are TSE's? Could the misfolded proteins be resistant to denaturation, thus could be transferred by medical instruments, dental instruments....?)...

    8. Antibiotics inhibiting bacterial protein synthesis: . examples include tetracycline, aminoglycosides, chloramphenicol, macrolides ( eg erythromycin) lincosamide, streptogramins

    9. Antiviral drugs: some drugs used to inhibit replication of viruses interfere with protein synthesis/processing eg antisense nucleic acids, protease inhibitors

    C. Nucleic Acids

    1. Polymers of nucleotides

    a. DNA= deoxyribonucleic acid; genetic information of cell

    b. RNA= ribonucleic acid: messenger, (mRNA), ribosomal (rRNA) and transfer (tRNA). Functions in transcription and translation of DNA base sequences into amino acid sequences of proteins

    2. Nucleotides: 3 components

    a. 5 C sugar + phosphate group + nitrogenous base (purine or pyrimidine)

    b. complementary base pairing A::T A::U C::G

    c. create a table to compare and contrast DNA to RNA

    DNA RNA

    sugar deoxyribose ribose

    phosphate + +

    nitrogenous bases adenine A adenine A

    thymine T uracil U

    guanine G guanine G

    cytosine C cytosine C

    Complementary base pairing

    A:::T A:::U

    G:::C G:::C

    #strands double stranded=ds single stranded=ss

    3. DNA , RNA: polymers of nucleotides joined by phosphodiester bonds. Hydrogen bonds between complementary bases hold 2 complementary sister DNA strands together (intermolecular H bonds) and stabilize complex 3-D shapes of RNA (intramolecular H bonds)

    4. a. Cells carry both DNA and RNA. In contrast, viruses carry either DNA or RNA, not both (some exceptions). There are some ssDNA viruses (parvovirus) and some ds RNA viruses (reoviruses) as well as ds DNA viruses and ssRNA viruses

    b. Most prokaryotes carry chromosomes of circular ds DNA; most eukaryotes carry multiple linear chromosomes made of ds DNA

    c. DNA can form complementary H bonds with RNA. This process is crucial in transcription (more later)

    d. To distinguish carbons in the 5 carbon sugar from the nitrogenous base carbons in a nucleotide, a “’” is added to the sugar carbons to distinguish them from the nitrogenous base carbons. Thus carbon 3’ or 5’ refers to carbons in the sugar and carbon 3 or carbon 5 refers to carbons in the nitrogenous base

    e. The combination of a 5 carbon sugar and a nitrogenous base is called a nucleoside. 1,2, or 3 phosphate groups made be added to the 5’ carbon creating nucleoside-mon-, di- or tri-phosphates

    f. Phosphates groups are attached to the 5’ carbon of the sugar in a nucleotide. In a growing strand of nucleic acid, incoming nucleotides may only be added at the 3’ OH end of the strand. Thus a strand is said to elongate in a 5’ to 3’ direction (5”->3’)

    g. If cut, a strand of DNA or RNA has a free 5’ phosphate end (5’P) and a free 3’OH end. In ds DNA, complementary “sister” strands are “antiparallel” in that the 5’ P end of one strand lies adjacent to the 3’OH end of the complementary sister strand

    h. Energized precursors required for synthesis of DNA/RNA are nucleoside triphosphates; in RNA/DNA strands, nucleoside monophosphate residues are present (more later)

    i. some antifungal drugs interfere with RNA function e.g. flurocytosine. Some antiprotozoan drugs inhibit nucleic acid synthesis/function: eflornithine, nitroimadazoles, pentamidine. Some antihelminthic drugs inhibit nucleic acid synthesis: niridazole, olitpraz, oxamniquine, all for Schistosoma infections

    i. Nucleoside triphosphates as energy sources: ATP: ATP is the “principle short-term, recyclable energy source for cells. Energy is stored in high energy bonds between phosphate groups 1~2 and 2~3 (~tilde indicates bind which releases large amounts of energy when hydrolyzed . More later in metabolism. Adenosine triphosphates is also a building block for RNA

    D. Carbohydrates: carbon + water/ generalized formula (CH2O)n. Energy storage, structural. C skeleton, carbonyl group, hydroxyl groups. Suffix “-ose” (see chem. homework sheet)

    1. types

    a. monosaccharides (=monomers) ex glucose, fructose, galactose, ribose, deoxyribose- structure of glucose & fructose . In aqueous solutions, glucose alternates between linear and ring forms. 2 ring forms depending on orientation of –OH on carbon 1, alpha and beta.

    -glucose is used as a source of energy and carbon

    b. disaccharides: ex sucrose (glucose + fructose), lactose (glucose + galactose)

    -glycosidic bonds join monosaccharide residues

    c. polysaccharides: polymers of monosaccharides; covalent bonds=glycosidic bonds. e.g. glycogen, starch (amylose + amylopectin)=polymers of alpha glucose; helical,some branched, cellulose = polymers of beta glucose; straight chains (know)

    2. Modified sugars e.g. modified glucose

    -NAG: addition of amino residue and acetyl group to carbon 2 of glucose forms

    N-acetylglucosamine (NAG)

    -chitin: polymer of beta-NAG; found in cell walls of fungi and exoskeleton of arthropods. Function similar to cellulose in plant cell walls

    -NAM: further modification of NAG to form N-acetylmuramic acid, NAM (lactic acid residue covalently linked to carbon3).. Only members of Domain Bacteria have enzymes to synthesize NAM, thus NAM is called a “signature” molecule” for Doman Bacteria

    -peptidoglycan: Unique to members of Domain Bacteria, found in bacterial cell walls, functions to strengthen cell walls and prevent osmotic lysis (similar to chitin and cellulose). Polymers of alternating NAG and NAM (“glycan” sugars) linked by beta glycosidic bonds crosslinked by peptide chains (“peptido”). Peptidoglycan/pg synthesis is the target of many antibiotics e.g. beta lactam antibiotics penicillin, ampicillin etc and vancomycin, cycloserine, bacitracin

    3. Hydrolysis of carbohydrates: an organism’s ability to use a carbohydrate as a carbon and energy source depends on its ability to synthesize hydrolytic enzymes specific for a carbohydrate

    carbohydrate

    Hydrolytic enzyme

    Lactose; milk sugar

    Mammalian “lactase”/bacterial “beta-galactosidase”

    Sucrose: ”table sugar”

    sucrase

    Maltose (breakdown product of starch)

    maltase

    cellulase

    cellulase

    4. Hydrolysis of glucose polymers by mammals: Mammals have enzymes to hydrolyze alpha glycosidic bonds between alpha glucose subunits found in starch and glycogen (e.g. salivary amylase). However mammals lack cellulase to hydrolyze beta glycosidic bonds found in cellulose, consequently mammals cannot digest plant cellulose (“fiber”).

    -Some herbivores (animals who eat plants) can digest cellulose-how?

    One group, the ruminants, have a 4 compartment “stomach” or digestive chamber which includes a rumen and reticulum. The rumen-reticulum are microbial fermentation vats filled with bacteria and protozoa. These microbes synthesize cellulase and hydrolyze cellulose the ruminants eat, releasing glucose subunits which can then be fermented. As a result of glucose fermentation, the microbes produce large amounts of carbon dioxide and methane (“greenhouse gases” released by “eructation”) and short chain fatty acids (C/energy source) and ammonium (absorbed across rumen wall into bloodstream). Rumen fluid then flows into the true stomach, the abomasum, for further digestion (note: the microbes themselves can act as nutrients). Thus the symbiotic relationship between ruminant and rumen microbe is mutualistic, both partners benefit.

    -Although horses and rabbits are not ruminants, their large ceca -(singular=cecum) contain cellulose digesting microbes and serve a similar function as the rumen-reticulum.

    -Of interest, rabbits are coprophagic, they eat their feces, thus benefiting from digestion of the cecal microbes passed in the feces.

    -recombinant cellulase made by E.coli:

    E. Lipids: primarily nonpolar, hydrophobic molecules

    1. Functions: important part of cell membranes, energy reserves, messenger molecules

    2. Two categories: fatty acid containing and fatty acid lacking

    a. fatty acid containing lipids;

    i.simple lipids= fats (aka triglycerides, triacylglycerol) fats=solid at room temperature; oils= liquids at room temp. Energy reserves.

    - fats/oils= glycerol + 3 fatty acids

    - fatty acid= carboxyl group + hydrocarbon tail (nonpolar, hydrophobic tail)

    -: fatty acids vary in #C’s in tail and presence of C=C double bonds

    (unsaturated fatty acids) or lack of C=C bonds (saturated fatty acids)

    ii. Complex lipids=phospholipids: glycerol + 2 fatty acids + phosphate + ‘R”

    - polar, hydrophilic “head” + nonpolar, hydrophobic “tail”

    - amphipathic/amphiphilic: contains both hydrophilic and hydrophobic regions

    - in aqueous solutions, phospholipids can spontaneously form phospholipid bilayers

    -selectively permeable

    -important component of cell membranes

    iii. waxes; fatty acids + alcohols. Acid-fast bacteria ‘AFB’s” such as Mycobacterium tuberculosis and Mycobacterium leprae (Hansen’s Disease/leprosy ) synthesize “waxy” cell walls (arabinogalactan-mycolic acid) which protect them against drying and chemicals such as disinfectants and antibiotics. As the hydrophobic waxy layer inhibits passage of antibiotics, people treated for TB/leprosy must take antibiotics for many months/years. AFB grow slowly in the lab and are hard to stain (require special “acid-fast” stain -more in lab). Isoniazid and ethambutol inhibit formation of the waxy cell wall layer.

    b. fatty acid -lacking lipids

    i. steroids=lipids composed of 4 HC rings + functional groups

    -. e.g. cholesterol; component of animal/protozoa cell membranes, precursor of hormones in animals (estrogen, testosterone, vitamin D

    -***not found in most bacteria (***exceptions ex Mycoplasma)

    - e.g. fungal sterols of cell membrane ex ergosterol.

    -target of polyene antifungal agents ex Nystatin. Amphotericin B

    -azole antifungal agents such as miconazole, fluconazole target fungal sterol synthesis

    Create summary charts (partially completed example below). Be able to identify molecules: amino aids, polypeptide, glucose, a glucose polymer, DNA, RNA, fat/oil, phospholipid, sterol. The only molecules you will be asked to draw from memory will be reaction between 2 amino acids forming dipeptide. Do chem. homework sheet posted on D2L

    Molecule

    Subunits

    Bonds

    Examples

    Functions

    Proteins

    amino acids

    peptide

    immunoglobulin

    enzymes, structural, transport, receptors

    Nucleic acids

    nucleotides

    phosphodiester

    DNA, RNA

    protein synthesis

    Lipids

    (nonpolar, hydrophobic)

    ester

    fats, oils

    energy stores, phospholipids, sterols, cell membrane

    Polysaccharides

    (example of carbohydrate)

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    General Microbiology: Bio 440 2015

    SCC Carberry

    Tortora Chapter 2: Chemistry Study guide/homework

    Note: this study guide is a tool (it works for some people but not for others). Make sure to master lecture/reading information first. Do chem worksheets passed out in lecture and posted on D2L .Read chapter 2. Answer questions at end of chapter 2

    ---------------------------------------------------------------------------------------------------------------------

    Ch 2 lecture: Basic organic chemistry

    Chemical bonds and attractive forces

    1. Which 4 elements are most commonly found in living organisms? (excluding skeleton). answer: “CHON”

    “ “ 6 elements? answer: CHONPS

    2. Describe:

    a. ionic bonds

    b. covalent bonds

    - nonpolar covalent bonds

    -polar covalent bonds

    - Given example of atoms involved in covalent bonds, be able to identify those which are polar, those which are nonpolar

    Examples below: Which form polar covalent bonds? Indicate which atoms have a partial negative or partial positive charge.

    O=O C-H O-H N-H H-H C-C

    c. hydrogen/H “bonds”

    d. Londen Dispersion Forces (old days “Van der Waals” forces) and hydrophobic

    molecules

    3. What is electronegativity? Rank the 4 elements most commonly found in organisms with respect to electronegativity.

    4. Note: we will skip the discussion of “CHEMICAL REACTIONS” until we reach Chapter 5, Metabolism

    5. : Special properties of Water:

    a. describe/draw the structure of water and its” hydrogen bonding” capacity. Recall polarity and hydrogen bond formation is one reason for water’s unusual properties

    b. describe some of the special/unusual properties of water for example:

    - moderation of temperature from high specific heat ( specific heat= the amount of heat which must be absorbed or lost for 1 gram of a substance to change its temperature by 1C) . “Heat is absorbed when hydrogen bonds break and heat is released when hydrogen bonds form. This helps keep temperature relatively steady within limits that permit life” Campbell Biology 8th edition p 56

    -evaporative cooling based on water’s high heat of vaporization.”The evaporative loss of the most energetic water molecules cools a surface.” Campbell Biology 8th edition p 56

    -cohesion: the binding together of like molecules, often by H bonds

    -adhesion: attraction between different types of molecules, often involves H bonds

    -the “solvent of life”: water is an excellent solvent because water molecules are attracted to charged and polar substances capable of forming hydrogen bonds”. Campbell.

    -water or its components participate in many cellular chemical reactions . examples: Hydrolysis and dehydration synthesis/condensation reactions

    6.a. What does hydrophobic and hydrophilic mean? examples?

    Which types of chemical bonds increase a molecule’s “hydrophilicity”?

    -hydrophobic

    -hydrophilic

    b. What does amphiphilic/amphipathic mean? examples?

    7. Why is carbon important in organic molecules? Why are organic molecules so diverse in structure and function? (hint: describe all the different carbon backbones/skeletons which can be formed)

    8. pH (More in lab)

    a.What is the “formula” for pH?

    b. A solution of pH1 has ____times more hydrogen ions than a solution of pH 2 (fill-in the blank)

    c. what is an acid? _______________________ a base? ______________________

    9. Be able to identify/label the functional groups discussed in lecture and classify as nonpolar, polar, hydrophilic, hydrophobic, acidic or basic. Which could form hydrogen bonds? Which group is involved in formation of disulfide bridges in proteins?

    Use the table below to organize your information: chem handouts or Ch 2 Powerpoint

    Name of group

    structure

    Properties: polar, nonpolar, hydrophilic, hydrophobic, acidic ,basic?

    examples

    Methyl

    hydroxyl/alcohol

    carbonyl

    -terminal=aldehyde

    -“internal”= ketone

    carboxyl

    amino

    ‘phosphoric acid residue” or “unionized phosphate” group

    sulfhydryl

    10. Diagram dehydration synthesis/condensation reactions vs hydrolysis. Condensation reactions and hydrolysis are usually catalyzed in cells by protein catalysts and RNA catalysts called __________ and ______ respectively (fill in blanks)

    11.a. Describe the 4 major groups of biologically important molecules.

    b.Be able to label the reactants and products associated with carbohydrates, nucleic acid, lipid and protein synthesis.

    c.Know monomeric subunits of protein, nucleic acid and polysaccharide polymers.

    d. In which would the following bonds be found? Peptide bonds, glycosidic bonds, phosphodiester bonds, ester bonds.

    (Note: creating a table to organize this information would be helpful. Fill-in the table below)

    Macromolecule

    (polymer)

    Subunits=monomers

    Covalent bonds formed

    Examples, functions

    Proteins/polypeptides

    Carbohydrates

    -polysaccharides

    Nucleic acids

    -DNA

    -RNA

    Note: Lipids are not polymers

    Lipids are not polymers

    Types of lipids:

    components

    Covalent bonds

    Examples functions

    Fats/triglycerides

    phospholipids

    Cell membranes

    Waxes

    Mycobacterium cell walls; Acid-fast bacteria

    Steroids/sterols

    Cholesterol; ergosterol in fungal membranes

    12. Understand the function/use of each general class of organic compound within the cell (carbohydrates/lipids/proteins/nucleic acids)

    Remember: Conformation =function!

    Amino acids and Proteins

    13.a Amino acids: be able to identify/draw and label the following parts of an amino acid: amino group, central carbon, H, carboxyl group, R side chain.

    b. If given the R group, be able to draw a specific amino acid.

    c. Which optical isomers/stereoisomers of amino acids are found in proteins?

    d. Where in nature may D optical isomers of amino acids be found?

    e.How many different amino acids are there found in proteins?

    f. Why are the R side chains important?

    g. Describe why the amino group may act as a base (decreases the H+ ion concentration in solution) and the carboxyl group can act as an acid (increases the H+ concentration in solution).

    h. What are amphoteric molecules?

    i. If given the structure of a R group, be able to determine if it would be hydrophobic or hydrophilic.

    14. Protein structure.

    a.How are amino acids joined together to form polypeptides?

    b. To which end of a polypeptide will new amino acids be joined?

    c. In a cell, which structures are responsible for forming polypeptides/proteins?

    d. Describe the 4 levels of protein structure:

    primary,

    secondary,

    tertiary

    and quaternary.

    e. Why is primary structure so important? (Remember that primary structure determines all other higher levels of protein structure).

    f. What does “functional conformation” mean?

    g. What determines the functional conformation of a protein

    h Within a globular cellular protein, where would one predict the hydrophobic amino acid residues would be located? The hydrophilic amino acid residues?

    i. What determines protein primary structure? (think DNA sequence of protein’s gene)

    15. If a mutation occurred in the gene for a globular protein such that the mutant protein had several hydrophobic amino acid residues in place of the “wild type” hydrophilic amino acid residues, how might the shape/conformation of the protein be altered? Effect on mutant protein function?

    16. Do all proteins have quaternary structure? Which levels of protein structure do immunoglobulins exhibit?

    17. Describe protein functions.

    18.a. Understand protein denaturation, its causes and significance.

    b. Which level of protein structure is usually maintained after denaturation?

    c. Why is denaturation usually irreversible?

    d.When is denaturation harmful? Beneficial? Practical applications?

    19. Protein folding diseases & prions

    a.Which microbial agent is extremely difficult to denature?

    b. Name examples of prion diseases and the consequences of “prion infection” (think TSE’s= __________________)

    Nucleotides and Nucleic acids

    20. Describe the 3 basic parts of DNA and RNA nucleotides.

    21.Create a chart comparing nucleotide composition of DNA vs RNA.

    22. Describe complementary base pairing of DNA vs RNA. (no abbreviations)

    23. Which nucleic acids are single stranded? double stranded?

    24. What does “antiparallel”, 5’ and 3’ ends mean?

    25. Label the parts of double stranded DNA including phosphodiester bonds.

    26. Why is DNA nucleotide base sequence important? Functions of DNA and RNA.

    27. Who discovered the structure of DNA?

    28.May RNA act as a organic catalyst? What are ribozymes? Describe one place in cells ribozymes are located.

    29. . What does “ATP” stand for? Why is it important? Describe 2 of its functions.

    Name of sugar

    Nitrogenous bases

    Complementary base pairs

    Double stranded ds or single stranded ss

    Phosphates present?

    DNA

    RNA

    Carbohydrates: monosaccharides, disaccharides, polysaccharides

    Monosaccharides

    30.What does the suffix “-ose” indicate?

    31. How many carbons are in glucose?

    32. Which functional groups are associated with glucose?

    33. Is glucose a polar, hydrophilic molecule? Can it form hydrogen bonds?

    34a. Be able to identify a glucose molecule in linear and ring forms.

    b.Be able to identify the alpha and beta forms of glucose in ring form.

    c. Which forms are found in glycogen, starch, cellulose?

    35. Functions of glucose in cell?

    36. Fructose is called a structural isomer of glucose. What does this mean?

    37.Be able to identify ribose and deoxyribose in ring forms. Where is each found in a cell? How many carbons are in these sugars?

    38. Name one hexose and one pentose.

    Disaccharides

    39a. Which monosaccharides combine to form the disaccharides maltose, lactose and sucrose?

    b. Function of each disaccharide?

    c. What is the specific name of the covalent bond which links monosaccharide residues in disaccharides/polysaccharides?

    d.Which enzymes are used to hydrolyze each of the 3 disaccharides mentioned above? e. (Of the 3 enzymes named above…) Which enzyme deficiency is found in many adult humans? Consequences? How might “probiotics” help these adults?

    Polysaccharides

    40a. Glycogen, starch and cellulose are all polysaccharides composed of______________(fill in the blank).

    b. Function of each polysaccharide?

    c. Which polysaccharide forms linear structures? Helical structures?

    d.Which of the above polysaccharides are formed by linkage of beta-glucose subunits? alpha-glucose subunits?

    e. Mammals lack enzymes to break the covalent bonds found in which of the above polysaccharides? (answer: cellulose) Which organisms make enzymes which can break these covalent bonds?( answer some bacteria, some protista) Name of these enzymes?(answer: “cellulases”).

    f. What are ruminants? Why can they “digest” cellulose found in plants?

    41. Modified carbohydrates:

    a.What are “NAG” and” NAM” and where are they found (be able to spell full names for quiz/exam)?

    b. Function?

    42.What is peptidoglycan?

    “”chitin?

    -Where are these found?

    -Which of the above mentioned molecules are “signature” molecules or are unique to bacteria?

    -Which of these molecules is/are found in the exoskeletons of crustaceans? fungal cell walls? bacterial cell walls?

    Lipids

    43.Which trait is common to all lipids?

    44. Fats/oils/triglycerides: a. Be able to identify glycerol, saturated and unsaturated fatty acids and a fat/oil molecule.

    b.-What is the name of the covalent bonds formed during a condensation reaction between glycerol and 3 fatty acids leading to formation of an oil/fat molecule?

    c.-What are products of hydrolysis of a fat/oil molecule. Functions of fats/oils?

    45. Phospholipids: a. Components of a phospholipid?

    b. Be able to identify a phospholipid molecule.

    c.Use a cartoon and label hydrophilic heads and hydrophobic tails.

    d. Why are phospholipids called “amphiphilic or amphipathic”?

    e. Explain how phospholipids react when placed in water..

    -Draw a phospholipid bilayer and a liposome and identify the hydrophobic core, hydrophilic heads and location of water molecules.

    -Explain how self assembly of phospholipid bilayers is important in formation of cell membranes.

    -What does “selectively permeable/semi-permeable” mean?

    -Describe the fluid mosaic model of cell membranes. What are the functions of membrane proteins?

    46. BONUS:In comparing 2 different bacteria, one adapted to life in cold Arctic waters, the other adapted to life in warm tropical waters, describe differences in the types of fatty acid residues found in the cell membrane phospholipids one would expect.

    47. Steroids: .Be able to identify the 4 carbon ring structure typical of steroids. Examples of steroids/sterols: cholesterol, ergosterol Vit D, cortisol, testosterone.

    48. Cholesterol is found in the cell membranes of __________. What is the function of cholesterol in cell membranes? Cholesterol is not found in the cell membranes of bacteria EXCEPT for some bacteria which lack cell walls ex Mycoplasma. How do Mycoplasma obtain their cholesterol?

    49.Ergosterol is found in the cell membranes of ________________ and is the target of 2 classes of antibiotics called ________________ and ___________________.

    50. Waxes: Significance of waxes in cell walls of Mycobacterium and “AFB’s”, Acid-Fast Bacteria?